miraligner video tutorial: miRNA annotation

miraligner command tool annotates sequences against miRBase database.

Read more about the options and outputs here: miraligner.sourceforge.net

Video tutorial for adapter removal command tool

SeqBuster Team has started a new serie of video tutorials for the available command tools.

The first one is dedicated to the adapter recognition and removal using adrec:

http://www.youtube.com/watch?v=0qGyAoG298M or

miraligner has a new html output

miraligner module, which annotates sequences to miRBase database, has a new html output format with a user-friendly dynamic table.

Update your version: svn update

Run miraligner and crossmapping.py(predict false positive miRNA hits) and you will obtain (the user can sort and search):

SeqCluster 10x faster

Our tool to annotate non-miRNA sequences is faster. We have improved the computer time to 1 hour/50.000 sequences (a normal set of sequences from a current run after miRNA annotation and filtering by 10 or more counts)

How to update

miraligner has an extra module to help with cross-mapping events

The problem when annotating miRNAs using only the miRBase database, it is that sometimes you could mis-annotate a sequence. An example: you have a sequence mapping onto a miRNA with a mismatch, but when you map against the genome, you find that the sequence has different perfect match. For that we coded crossmapping.py, which uses the output of miraligner and gives you a clue about when a miRNA could be mis-annotated.

Read more here:

miraligner wiki

Minor bug detected when limiting frequency parameter

Minor bug detected in the miRNA analysis when the user limit the frequency parameter. The user obtained a error or not output.
To update, please, type inside the "seqbuster" folder:

svn update


Thanks to users for the feedback

minor changes released in miraligner, adrec and seqbuster. to update, type: svn update.

The different updates:

miraligner: when call the program without arguments, Usage will be prompted

adrec: the number of lines read print during the process, are now written in the same position

seqbuster: the width of the species option in the miRNA detection has been changed to allow better visualization

To update, type inside the tool folder: svn update

Thanks to use SeqBuster pack